R/methods-updateObject.R

In roryk/bcbioSinglecell: Single-Cell RNA-Seq Utilities

#' Update an Object to Its Current Class Definition
#'
#' @name updateObject
#' @family S4 Object
#' @author Michael Steinbaugh
#'
#' @inherit BiocGenerics::updateObject
#'
#' @importFrom BiocGenerics updateObject
#'
#' @return `bcbioRNASeq`.
#'
#' @examples
#' # bcbioSingleCell ====
#' updateObject(indrops_small)
NULL



# Methods ======================================================================
#' @rdname updateObject
#' @export
setMethod(
    "updateObject",
    signature("bcbioSingleCell"),
    function(object) {
        version <- slot(object, "metadata")[["version"]]
        assert_is_all_of(version, c("package_version", "numeric_version"))
        message(paste("Upgrading from", version, "to", packageVersion))

        # Coerce to SingleCellExperiment
        sce <- as(object, "SingleCellExperiment")

        # Assays ===============================================================
        assays <- slot(sce, "assays")
        # Coerce ShallowSimpleListAssays to list
        assays <- lapply(seq_along(assays), function(a) {
            assay <- assays[[a]]
            assert_are_identical(colnames(assay), colnames(sce))
            assay
        })
        names(assays) <- assayNames(sce)

        # raw counts
        if ("raw" %in% names(assays)) {
            message("Renaming `raw` assay to `counts`")
            assays[["counts"]] <- assays[["raw"]]
            assays[["raw"]] <- NULL
        }

        assays <- Filter(Negate(is.null), assays)
        # Put the required assays first, in order
        assays <- assays[unique(c(requiredAssays, names(assays)))]
        assert_is_subset(requiredAssays, names(assays))

        # Column data ==========================================================
        # Ensure that all `sampleData` columns are now slotted in `colData`
        colData <- colData(sce)
        sampleData <- metadata(sce)[["sampleData"]]
        assert_is_data.frame(sampleData)
        cell2sample <- cell2sample(sce)
        assert_is_factor(cell2sample)
        colData[["cellID"]] <- rownames(colData)
        colData[["sampleID"]] <- cell2sample
        sampleData[["sampleID"]] <- rownames(sampleData)
        colData <- merge(
            x = colData,
            y = sampleData,
            by = "sampleID",
            all.x = TRUE
        )
        rownames(colData) <- colData[["cellID"]]
        colData[["cellID"]] <- NULL
        sampleData[["sampleID"]] <- NULL

        # Metadata =============================================================
        metadata <- metadata(sce)

        # version
        metadata[["previousVersion"]] <- metadata[["version"]]
        metadata[["version"]] <- packageVersion

        # Return ===============================================================
        .new.bcbioSingleCell(
            assays = assays,
            rowRanges = rowRanges(sce),
            colData = colData,
            metadata = metadata
        )
    }
)